Here's the right direction: Devel::DProf (or Apache::DProf for mod_perl). That will tell you which part of your application is slow.

The most common cause of performance problems in simple web systems is database performance, often due to poor table design or inefficient SQL. You can use DBIx::Profile to find slow SQL statements that need to be fixed.

Of course, before you do anything else you should make sure that your machines have enough RAM and are not swapping. The mod_perl guide you mentioned can help you deal with that.